Effects of mutations

V. EFFECTS OF MUTATIONS

V A. POTENTIAL EFFECTS OF MUTATIONS

Mutations in translated regions:

Base substitution mutations

Wild-type (sometimes termed "samesense"): where the base substitution mutation causes the same amino acid to be inserted as was found in wild-type. (Though such a mutation will probably not affect the phenotype, it just might through: effects on DNA structure, sites for DNA modification, sites involved in mRNA synthesis, sites necessary for mRNA stability or instability because of binding of protective or degradative proteins, changes in mRNA structure, and effects on translation through changes in codon choice or context).

Non-wild-type (missense mutations): where the base substitution mutation causes an amino acid to be inserted which differs from that in a wild-type protein. This can give rise to normally active proteins, inactive proteins, less active proteins, unstable proteins (where the protein is prematurely degraded by proteases within the cell), conditionally active proteins (where the conditional step is either at the level of protein stability or protein synthesis), hyperactive proteins, proteins with new function, charge-altered proteins, proteins that are unprocessed (e.g. where processing is required for insertion into or extrusion through the membrane), and finally longer proteins (where the termination signal itself is altered). The typical result will be a less functional product.

Nonsense mutations yield shortened polypeptides that typically have little or no activity and tend to be highly unstable because of intracellular proteases. Such mutations often display some polarity onto transcriptionally downstream genes. In bacteria, UAA (a.k.a. ochre), UAG (a.k.a. amber), and UGA (a.k.a. opal) are usually recognized as stop signals.

Frameshift mutations: These tend to have a profound effect on a protein product including both loss of function and instability. Since frameshift mutations put ribosomes out of the proper reading frame, they often disclose nonsense codons which then result in polarity.

(The above-described mutations are referred to collectively as "point" mutations.)

Small deletions: These will typically give a complete loss of protein function and cause proteins to be synthesized that are of less than normal stability. Approximately two-thirds of such small deletions (if internal to a gene) will be polar to some extent onto downstream genes.

Mutations in untranslated regions:

Transcribed: Mutations that occur in transcribed but untranslated regions might still affect the translation system by affecting the recognition signal for binding of ribosomes. They might conceivably affect mRNA stability, attenuation, and, where the gene product is an RNA, mutations might cause a loss of product function or cause improper processing or modification of the product.

Untranscribed regions: Mutations in regions that are neither transcribed nor translated might affect either transcriptional start or stop signals and thus the regulation of the region in question. It is also possible they might affect "structural" regions of the DNA, affecting gene expression indirectly.

Large deletions, inversions, and duplications: Such mutations can span both translated and transcribed regions and as such they can have a variety of effects. For example, they can generate transcript fusions or gene fusions; they can generate strong polarity; and deletions and inversions typically eliminate the products of the affected genes. Large inversions also have the subtle effect of changing gene position with respect to the origin of replication, thus changing the average copy number per cell. Duplications can have phenotypes when the copy number of that particular region is critical.

Insertions, insertion sequences, and transposons: Mutations involving such mechanisms will destroy whatever function was encoded by the affected region. They typically cause polarity due to their encoding of RNA termination signals and can occasionally provide new promoters reading into the flanking regions.

V B. NUMEROLOGY

numerology: 1. a system of occultism built around numbers...; 3. divination by numbers.

One of the central themes of this course is that the frequency at which events occur makes predictions as to their type. To put it another way, phenotypes which appear frequently must occur by either (l) any of a large number of infrequent genome alterations or (2) a particular, very frequent genome alteration. The frequency of events determines the mode of analysis necessary in order to determine them. Ignoring hot spots, the following list gives an approximate idea of the sorts of frequencies with which various sorts of events occur:

very frequent:

loss of various plasmid types- 10-2 - 10-3

loss of tandem duplication - l0-l - 10-2 (by recA gene product)

occurrence of a duplication of a given region - 10-3

site-specific recombination events - 10-1 - 10-2

frequent:

spontaneous "knockout" of a gene - 10-5

transposition of a Tn to new site - 10-4 - 10-7

detectable:

typical spontaneous reversion frequency of a frameshift

missense or nonsense mutation - 10-6 - 10-8

precise excision of a transposon - 10-6 - 10-9

spontaneous deletions - 10-5 - 10-7

transposition of a Tn to a particular site - ?

Obviously, the above table is a bit deceptive. For example, it has already been stated that some insertion sequences revert at a reasonable frequency and some scarcely revert at all. On the other hand, if an event is occurring at 10-2 frequency, you may safely assume that it does not involve the occurrence of some very particular base substitution mutation since such events are simply too rare. It must involve a loss of a plasmid or something to do with duplications since these are the major events in bacteria which can occur at that frequency. Similarly, if a phenotype is occurring at very low frequency, then you may assume it is not arising by some reasonably common event like the loss of a plasmid or the knockout of a gene, but rather by some very specific base substitution or base change of some sort. The frequency of an event reflects both the likelihood of the mutational mechanism as well as the target size for events which cause the desired phenotype.